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Question: My Female subjects seem to be expressing Y Chromosome Genes
1
gravatar for e.whittle
2.5 years ago by
e.whittle • 10
e.whittle • 10 wrote:

Hi,

I have recently sequenced extracted RNA from plasma samples taken from female subjects. Upon analysis using CuffDiff I discovered that galaxy had detected RNA that matched up to a number of Y chromosome genes. As my subjects are all females, and thus should not possess Y chromosomes I have been trying to figure out how this occurred. I was, therefore, wondering if these results were due to misalignment of the sequenced reads to the reference genome, and thus was wondering the best way to determine read coverage of the genes using Galaxy. Would really appreciate any help anyone can give

Emma
alignment galaxy read coverage cuffdiff • 690 views
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written 2.5 years ago by e.whittle • 10
3
gravatar for michalovova.monika
2.5 years ago by
michalovova.monika • 50
United States
michalovova.monika • 50 wrote:

Are these human samples? X and Y chromosome share a region with relatively high degree of homology called X-degenerate region. As a consequence, some genes have both X and Y variants (e.g. AMELX on X chromosome and AMELY on Y chromosome). Moreover, even highly diverged regions of the Y chromosome will sometimes have genes with both X and Y versions (e.g. VCX and VCY) or even with the autosomal versions. It is therefore important to know exactly which reference you are using. Extremely tiny amounts of mapping to Y chromosome could also be results of a microchimerism (when an individual is chimera or as an result of a pregnancy with the male offspring). Do all your female subjects have these mappings? How much their levels vary?

ADD COMMENT • link written 2.5 years ago by michalovova.monika • 50
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